I'm using DynoSim Pro Tools and so far it looks to be low by about 2 1/2%. If I track 400, actual from dyno results is 410. This software was regularly $250, but is currently on sale for 99 bucks. I'm using 0.006" tappet lift for the seat-to-seat figures, so maybe if I stretched it out a couple of degrees on each side to cover the seat to seat figures, I might be right on the money.

Mooneye hit the nail on the head. Even if the software is off a bit, it will tell you which way to go with changes. Like I said on another thread here, I picked up 55 ft/lbs of torque and 90 hp for a fellow on another forum with a manifold and header change.